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UKAEA-Edge-Code
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Extending the kinetic mesh beyond the BOUT++ plasma domain
- #44
#44
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mrhardman
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VANTAGE-Reactions-Coupling/dev
UKAEA-Edge-Code/hermes-3:VANTAGE-Reactions-Coupling/dev
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VANTAGE-Reactions-Coupling/dmplex-features
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Extending the kinetic mesh beyond the BOUT++ plasma domain
#44
mrhardman
wants to merge 45 commits into
VANTAGE-Reactions-Coupling/dev
UKAEA-Edge-Code/hermes-3:VANTAGE-Reactions-Coupling/dev
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VANTAGE-Reactions-Coupling/dmplex-features
UKAEA-Edge-Code/hermes-3:VANTAGE-Reactions-Coupling/dmplex-features
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Commits on Aug 3, 2026
For the `particle_animator.py` script, use the length normalisation stored in the BOUT.dmp.*.nc files to plot the particle positions in SI units, following the change to normalised units in the van…
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Initial changes to load a mesh from a GMSH .msh file in serial, and then distribute this over MPI ranks. Tested only in serial. Prototype code for MPI map information for DG0 object is left in place.
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Commits on Aug 13, 2026
Define `use_external_msh` in the VANTAGE class to allow the same flag to determine how dg0 is created (in a later commit).
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Commits on Aug 14, 2026
Move definition of dg0 pointer to vantage header file, introduce sketch of code to make the `mesh_coupler_dg0` variable.
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Make separate function for writing the DMPlex to HDF5.
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Use a c++ style static cast in `DMPlexCreateGmshFromFile()`.
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Restructure `vantage_dmplex.cxx` so that `create_dmplex_from_Bout_mesh()` and `create_dmplex_from_GMSH_msh()` are separate functions for initialising the DMPlex. For now, always use the `project_ev…
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Make `kinetic_mesh_map` a class variable, read in map to global index of triangles in kinetic grid.
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Commits on Aug 18, 2026
Add Rxy, Zxy, and corner variables to the BOUT.dmp.vantage.*.nc output files.
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Commits on Aug 21, 2026
Set xlim based on command-line argument.
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Use forward and backward tranfers in conversion from NESO-Particles degrees of freedom to BOUT++ Field2D data when the kinetic mesh has a different number of degrees of freedom to the BOUT++ grid. …
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Commits on Aug 24, 2026
Extend the kinetic -> bout mesh data transfer to the VantageSourceManager.
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Refactor the inputs of the [vantage] component so that pressure and temperature are inputs. The initial condition is a uniform Maxwellian across the entire kinetic domain. Propagate the temperature…
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Commits on Aug 28, 2026
Experiments using .vtkhdf for prototype velocity-moment diagnostics on the kinetic mesh.
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Create function to contain kinetic moment diagnostic code.
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Update derived diagnostics moment kernels before projection.
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Calculate the Gamma = nu mean flow moment in the kinetic diagnostics.
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Refactor diagnostics calculation to enable the calculation of derived moments such as pressure and temperature.
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Commits on Sep 4, 2026
Merge branch 'VANTAGE-Reactions-Coupling/dev' into VANTAGE-Reactions-Coupling/dmplex-features
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Commits on Sep 7, 2026
Extend checks on cell volumes to cover the case where the kinetic mesh is externally supplied.
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Commits on Sep 8, 2026
Ensure that `y_boundary_guards` is saved to that the `BOUT.dmp.vantage.0.nc` output file can be used as a valid grid file when produced by a hermes-3 simulation running in serial.
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Begin refactoring diagnostics so that they are managed through a class VantageDiagnosticsManager.
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Commits on Sep 9, 2026
Split kinetic diagnostic function into update and write functions.
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Initial move of BOUT++ style diagnostic functions to VantageDiagnosticsManager class.
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Extract BOUT++ Field2D from the computed scalar variable diagnostics on the kinetic mesh.
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Commits on Sep 10, 2026
Split VantageSourceManager class to separate file to speed up compilation in parallel. Rename `source_data` variable to `source_data_plasma_grid`.
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Add a vector to store source data on the kinetic mesh.
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Define get functions for plasma grid and kinetic mesh data.
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Changes aimed to allow testing of mass conservation when the kinetic mesh covers a larger physical volume than the plasma grid. Plasma quantities (set from inputs) are temporarily extended to the k…
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Commits on Sep 11, 2026
Make VantageDataTransfer class to handle the transfer of data between Field2D, std::vector and particle groups. Correct bug in ASSERT1() in vantage_sources.cxx.
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Use VantageDataTransfer in VantageSourceManager.
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Changes to initialise the plasma properties on Field2D on the BOUT++ grid, and to transfer this data first to the kinetic mesh and then to the particle group with functions from the VantageDataTran…
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Commits on Sep 14, 2026
Fix bug in `VantageDataTransfer::transfer_scalar_to_kinetic_mesh`.
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Commits on Sep 15, 2026
Make the particle group variable passed as an arguement to enable the data transfer functions to act on multiple particle groups for the same mesh.
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Introduce particle sub groups which ensure neutral-plasma reactions are only applied when the electron density is greater then the `electron_density_reaction_threshold` input parameter. Set the mar…
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Modify the diagnostics so that the sources are written to both kinetic mesh and plasma grid diagnostics, through a for loop indexing over the existing sources in the source manager object. Only sca…
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Attempt to calculate total mass for mass conservation check using the Field2D for the ion_density. Fails mass conservation test for the cases where the kinetic mesh extends beyond the BOUT++ mesh b…
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Commits on Sep 17, 2026
Fix mass conservation test by using the correct summation of neso_mesh cell volumes, transferred from the kinetic mesh to plasma grid using unit weights so that the areas of triangles in the kineti…
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Confirm that mass is conserved (in a slab) when density is computed from the sources stored in Field2D format.
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Write out neso_cell_volumes -> neso_cell_areas as BOUT++ Field2D, use this field in the `particle-pusher/runtest` to diagnose mass conservation.
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Test the sum of neutral mass and ionised mass by summing over sources.
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Commits on Sep 21, 2026
Support non-rectangular BOUT++ plasma grid cells, by computing the relative area of the two kinetic mesh triangles which subdivide the plasma quadrilateral cell.
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Commits on Sep 22, 2026
Refactor particle-pusher/runtest so that simulation directory is specified once.
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Include a .msh file and necessary data to generate a valid bout.grd.nc input grid file for a test of the extended kinetic mesh implementation in a slab case. The test uses the the `tests/integrated…
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Use fewer x, y cells in the test of particle pushing on quad cells aligned with a BOUT++ grid. Achieves a speedup in the test runtime.
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